| Age | Commit message (Expand) | Author |
|---|
| 2022-05-12 | gnu: fastahack: Wrap long line....* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
| Arun Isaac |
| 2022-05-11 | gnu: cwltool: Do not propagate inputs....* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ...
[inputs]: ... here.
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Set absolute path to pkg-config....Setting the absolute path to pkg-config is required to support
cross-compilation.
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set
PKG_CONFIG_EXECUTABLE in #:configure-flags.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Find submodule sources in native-inputs during cross-compilation....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In the
unpack-submodule-sources phase, look for submodule sources in both inputs and
native-inputs.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Use G-expressions....* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using
G-expressions.
[arguments]: Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: fastahack: Use compiler specific to the build target....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Set CXX in
#:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: fastahack: Use G-expressions....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Rewrite
using G-expressions. Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Fix cross-compilation....tabixpp links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and
xz should be listed in inputs even though they are already present implicitly
in native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (tabixpp)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use build tools specific to the target....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Set CC and CXX in
#:make-flags. In the build-libraries phase, use cxx-for-target instead of g++
and ar-for-target instead of ar.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use #:make-flags....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the
build phase. Move the required make arguments to #:make-flags. Add
build-libraries phase.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use G-expressions....* gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent.
[arguments]: Use search-input-file and search-input-directory.
[source, arguments]: Rewrite using G-expressions. Do not return #t from
snippets and custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-06 | gnu: pigx-sars-cov-2: Update to 0.0.7....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
| Ricardo Wurmus |
| 2022-05-06 | gnu: Add pigx-sars-cov-2....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
| Ricardo Wurmus |
| 2022-05-02 | gnu: python-hic2cool: Fix build....* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
| Ricardo Wurmus |
| 2022-05-02 | gnu: htslib-for-stringtie: Inherit from htslib-1.12....* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
| Ricardo Wurmus |
| 2022-05-02 | gnu: python-cooler: Use more recent cytoolz....* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
| Ricardo Wurmus |
| 2022-04-26 | gnu: Add r-giotto....* gnu/packages/bioinformatics.scm (r-giotto): New variable.
| Ricardo Wurmus |
| 2022-04-19 | gnu: vcflib: Update to 1.0.3....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
| Efraim Flashner |
| 2022-04-14 | gnu: scregseg: Remove cythonized file....* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
| Efraim Flashner |
| 2022-04-14 | gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics)....* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
| Ricardo Wurmus |
| 2022-04-11 | gnu: Add r-copykat....* gnu/packages/bioinformatics.scm (r-copykat): New variable.
| zimoun |
| 2022-04-10 | gnu: smithwaterman: Fix cross-compiling....The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More
closely match the 'ar' and 'ld' commands when substituting them.
| Efraim Flashner |
| 2022-04-06 | gnu: Add r-rnaseqdtu....* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Hong Li |
| 2022-04-05 | gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR....This is needed since the update of python-loompy.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.
| Ricardo Wurmus |
| 2022-04-05 | gnu: pigx-scrnaseq: Use new inputs style....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
| Ricardo Wurmus |
| 2022-04-05 | gnu: pigx-scrnaseq: Update to 1.1.8....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-04-04 | gnu: freebayes: Fix test suite....* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
| Efraim Flashner |
| 2022-04-04 | gnu: smithwaterman: Use new style for phases....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
| Efraim Flashner |
| 2022-04-04 | gnu: smithwaterman: Fix cross-compiling....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.
| Efraim Flashner |
| 2022-03-31 | gnu: python-velocyto: Set cache directory for Numba....* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
| Ricardo Wurmus |
| 2022-03-31 | gnu: wfmash: Enable test suite....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
| Efraim Flashner |
| 2022-03-31 | gnu: Add wfmash....* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-03-31 | gnu: htslib: Add bzip2 and xz to inputs....htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-03-31 | gnu: python-loompy: Update to 3.0.7....* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
| Ricardo Wurmus |
| 2022-03-29 | gnu: r-signac: Update to 1.6.0-2.458e647....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2022-03-29 | gnu: plink-ng: Update to 2.00a3-20220315....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
| Ricardo Wurmus |
| 2022-03-29 | gnu: Add r-cytobackbone....* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2022-03-29 | gnu: pigx-sars-cov2-ww: Update to 0.0.5....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-03-29 | gnu: pigx-rnaseq: Update to 0.0.20....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-03-09 | gnu: Add r-scopeloomr....* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
| Ricardo Wurmus |
| 2022-03-02 | gnu: texlive-latex-pgf: Rename to "texlive-pgf"....Suggested by Ricardo Wurmus.
* gnu/packages/tex.scm (texlive-latex-pgf): Rename to...
(texlive-pgf): ... this. Change 'name' accordingly.
(texlive-latex-pgf): Define as deprecated.
(texlive-beamer)[propagated-inputs]: Use the new name.
(texlive-todonotes)[propagated-inputs]: Likewise.
(texlive-adjustbox)[propagated-inputs]: Likewise.
(texlive-tcolorbox)[propagated-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
| Ludovic Courtès |
| 2022-02-27 | gnu: minimap2: Update to 2.24....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
| Efraim Flashner |
| 2022-02-22 | gnu: Add r-dyngen....* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
| Ricardo Wurmus |
| 2022-02-15 | gnu: python-gffutils: Update to 0.10.1....* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase. Respect TESTS? in check phase while at
it.
| Marius Bakke |
| 2022-01-31 | gnu: Add scvelo....* gnu/packages/bioinformatics.scm (scvelo): New variable.
| Ricardo Wurmus |
| 2022-01-31 | gnu: python-louvain-0.6: Update to 0.7.1....* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1.
[arguments]: Add build phases 'find-igraph and 'pretend-version.
[native-inputs]: Add python-setuptools-scm and python-wheel.
Rename this variable...
(python-louvain-0.7): ...to this, naturally.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update
reference to python-louvain-0.6.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Remove trailing #T from build phase....* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Update to 0.2.3....* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-sars-cov2-ww: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set
PYTHONPATH variable in new build phase.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-scrnaseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
| Ricardo Wurmus |
